Then it seems to me that you are just relying on a peculiarity of the Ada build system, that is the fact that you can work entirely from within the GCC directory.
That's by design, of course. What you need to do then, is to run from the toplevel "make stage3-bubble; make -C gcc gnatlib_and_tools". Does the latter differ from "cd gcc; make gnatlib_and_tools"?